Abstract

The current human mitochondrial (mtDNA) phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poorly represented, suggesting that extensive hidden phylogenetic substructure remains to be uncovered. This study expanded and re-analysed the available datasets of I and W complete mtDNA genomes, reaching a comprehensive 419 mitogenomes, and searched for precise correlations between the ages and geographical distributions of their numerous newly identified subclades with events of human dispersal which contributed to the genetic formation of modern Europeans. Our results showed that haplogroups I (within N1a1b) and W originated in the Near East during the Last Glacial Maximum or pre-warming period (the period of gradual warming between the end of the LGM, ∼19 ky ago, and the beginning of the first main warming phase, ∼15 ky ago) and, like the much more common haplogroups J and T, may have been involved in Late Glacial expansions starting from the Near East. Thus our data contribute to a better definition of the Late and postglacial re-peopling of Europe, providing further evidence for the scenario that major population expansions started after the Last Glacial Maximum but before Neolithic times, but also evidencing traces of diffusion events in several I and W subclades dating to the European Neolithic and restricted to Europe.

Conflict of interest statement

Competing Interests: Author Scott R. Woodward is employed by the commercial company AncestryDNA, Provo, UT. After having carefully read the journal's policy, the authors confirm that this does not alter their adherence to all the PLOS ONE policies on sharing data and materials. They confirm that Alessandro Achilli is a PLOS ONE Editorial Board member. After having carefully read the journal's policy, the authors confirm that this does not alter their adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1. Phylogenetic tree of haplogroups N1a1b…

Figure 1. Phylogenetic tree of haplogroups N1a1b and W.

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This schematic representation is based on…

Figure 1. Phylogenetic tree of haplogroups N1a1b and W.

This schematic representation is based on 196 N1a1b and 223 W mitogenomes whose phylogenetic relationships are illustrated in detail in Figure S1 and Figure S2. The phylogenetic connections between N1a1b and W are also shown. Approximate ages can be inferred from the scale. For haplogroups N1a1b and W, they correspond to the ML ages in Table 1 while previously reported ML ages were employed for nodes N, N1 and N2 .

Figure 2. Spatial frequency distribution of haplogroups…

Figure 2. Spatial frequency distribution of haplogroups I and W and the sub-clades I1a and…

Figure 2. Spatial frequency distribution of haplogroups I and W and the sub-clades I1a and W6.

Note that different frequency scales (%) were used in the maps. The dots in the lower map indicate the geographic location of the population samples included in the survey (Table S3 in File S1).

Figure 3. Bayesian Skyline Plots (BSPs) of…

Figure 3. Bayesian Skyline Plots (BSPs) of haplogroups N1a1b and W.

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Hypothetical effective population sizes…

Figure 3. Bayesian Skyline Plots (BSPs) of haplogroups N1a1b and W.

Hypothetical effective population sizes through time are based on the mitogenomes listed in Table S1 and Table S2 (File S1).

Grant support

This research received support from the Leverhulme Trust (research project grant 10 105/D)(to MBR), the Sorenson Molecular Genealogy Foundation (to UAP and SRW) and the Italian Ministry of Education, University and Research: Progetti Futuro in Ricerca 2008 (RBFR08U07M) and 2012 (RBFR126B8I) (to AA and AO) and Progetti Ricerca Interesse Nazionale 2009 and 2012 (to AA, AT and OS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.